2013
DOI: 10.1093/nar/gkt1300
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Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

Abstract: Recent sequencing technologies that allow massive parallel production of short reads are the method of choice for transcriptome analysis. Particularly, digital gene expression (DGE) technologies produce a large dynamic range of expression data by generating short tag signatures for each cell transcript. These tags can be mapped back to a reference genome to identify new transcribed regions that can be further covered by RNA-sequencing (RNA-Seq) reads. Here, we applied an integrated bioinformatics approach that… Show more

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Cited by 17 publications
(13 citation statements)
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References 33 publications
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“…Serial analysis of gene expression (SAGE) : targets polyadenylated messages and generates a single internal (typically close to the 3′ end) tag per RNA molecule [145]. …”
Section: The Non-coding Rna Universementioning
confidence: 99%
“…Serial analysis of gene expression (SAGE) : targets polyadenylated messages and generates a single internal (typically close to the 3′ end) tag per RNA molecule [145]. …”
Section: The Non-coding Rna Universementioning
confidence: 99%
“…In this approach, early barcoding and multiplexing allow the preparation and sequencing of an extensive number of samples at once, hereby strongly reducing the sequencing cost per sample. Briefly, fragmented polyadenylated RNA molecules are used as a template for reverse transcription, resulting in a library that merely contains the 3′‐end of all polyadenylated RNA molecules, including mRNA transcripts as well as micro‐RNAs (miRNA) and other non‐coding RNAs [Philippe et al ., ; Figures and a, b and Method S1]. Consequently, this method is able to reveal the location of 3′‐ends of all polyadenylated transcripts in each sample.…”
Section: Introductionmentioning
confidence: 99%
“…; Necsulea & Kaessmann ; Philippe et al . ). The Cufflinks‐predicted exons mapped to the genome were first merged across the three tissues within each individual using Cuffmerge and then intersected across groups of individuals using bedtools v 2.19.1 (Quinlan & Hall ) to reveal the following four groups: (i) exons common to all males for the comparison of RNA‐seq and DNA‐seq variants in the single reference male, (ii) exons common to all individuals, (iii) exons common to all females (but not found in all males) and (iv) exons common to all males (but not found in all females).…”
Section: Methodsmentioning
confidence: 97%
“…Parsimonious sets of transcripts for each tissue type were assembled using CUFFLINKS v2.1.1 (Trapnell et al 2010; Appendix S1, Supporting information). This step provides a complete picture of the transcriptome, because it takes the untranslated regions of genes into account, and considers differential splicing and poly-adenylated long noncoding RNA and miRNA precursors (Guttman et al 2009;Necsulea & Kaessmann 2014;Philippe et al 2014). The Cufflinks-predicted exons mapped to the genome were first merged across the three tissues within each individual using Cuffmerge and then intersected across groups of individuals using BEDTOOLS V2.19.1 (Quinlan & Hall 2010) to reveal the following four groups: (i) exons common to all males for the comparison of RNA-seq and DNA-seq variants in the single reference male, (ii) exons common to all individuals, (iii) exons common to all females (but not found in all males) and (iv) exons common to all males (but not found in all females).…”
Section: Transcriptome Mapping and Assemblymentioning
confidence: 99%